Package | Description |
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com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
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com.compomics.util.experiment.identification.protein_sequences |
Protein sequence handling related classes.
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com.compomics.util.gui.parameters.identification_parameters |
GUI classes for parameters, settings and preferences used for identification.
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com.compomics.util.preferences |
Utilities preferences classes.
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Constructor and Description |
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FMIndex(WaitingHandler waitingHandler,
boolean displayProgress,
PeptideVariantsPreferences peptideVariantsPreferences,
SearchParameters searchParameters)
Constructor.
|
FMIndex(WaitingHandler waitingHandler,
boolean displayProgress,
PtmSettings ptmSettings,
PeptideVariantsPreferences peptideVariantsPreferences)
Constructor.
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Modifier and Type | Method and Description |
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PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean displayProgress,
int nThreads)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
Modifier and Type | Method and Description |
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PeptideVariantsPreferences |
PeptideVariantsSettingsDialog.getPeptideVariantsPreferences()
Returns the peptide variants settings as set by the user.
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Constructor and Description |
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PeptideVariantsSettingsDialog(Dialog owner,
Frame parentFrame,
PeptideVariantsPreferences peptideVariantPreferences,
boolean editable)
Creates a new FractionSettingsDialog with a dialog as owner.
|
PeptideVariantsSettingsDialog(Frame parentFrame,
PeptideVariantsPreferences peptideVariantPreferences,
boolean editable)
Creates a new FractionSettingsDialog with a frame as owner.
|
Modifier and Type | Method and Description |
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static PeptideVariantsPreferences |
PeptideVariantsPreferences.getNoVariantPreferences()
Returns the preferences corresponding to no variants allowed.
|
PeptideVariantsPreferences |
IdentificationParameters.getPeptideVariantsPreferences()
Returns the peptide variant preferences.
|
Modifier and Type | Method and Description |
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boolean |
PeptideVariantsPreferences.isSameAs(PeptideVariantsPreferences peptideVariantsPreferences)
Indicates whether another peptide variant preferences is the same as this
one.
|
void |
IdentificationParameters.setPeptideVariantsPreferences(PeptideVariantsPreferences peptideVariantsPreferences)
Sets the peptide variant preferences.
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Constructor and Description |
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IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationSettings annotationSettings,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideVariantsPreferences peptideVariantsPreferences,
GenePreferences genePreferences,
PsmScoringPreferences psmScoringPreferences,
PeptideAssumptionFilter peptideAssumptionFilter,
PTMScoringPreferences ptmScoringPreferences,
ProteinInferencePreferences proteinInferencePreferences,
IdMatchValidationPreferences idValidationPreferences,
FractionSettings fractionSettings)
Constructor.
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